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(-) Description

Title :  CRYSTAL STRUCTURE OF A HYPOTHETICAL ADP-DEPENDENT PHOSPHOFRUCTOKINASE FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  A. H. Y. Wong, Z. Jia, T. Skarina, J. R. Walker, C. Arrowsmith, A. Joachim A. Edwards, A. Savchenko, Midwest Center For Structural Genomic
Date :  20 Jul 04  (Deposition) - 14 Sep 04  (Release) - 17 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Adp-Pfk, Pyrococcus, Midwest Center For Structural Genomics, Apc5054, Protein Structure Initiative, Psi, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Currie, F. Merino, T. Skarina, A. H. Wong, A. Singer, G. Brown, A. Savchenko, A. Caniuguir, V. Guixe, A. F. Yakunin, Z. Jia
Adp-Dependent 6-Phosphofructokinase From Pyrococcus Horikoshii Ot3: Structure Determination And Biochemical Characterization Of Ph1645.
J. Biol. Chem. V. 284 22664 2009
PubMed-ID: 19553681  |  Reference-DOI: 10.1074/JBC.M109.012401

(-) Compounds

Molecule 1 - ADP-SPECIFIC PHOSPHOFRUCTOKINASE
    ChainsA, B
    EC Number2.7.1.146
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET15B
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificPYROCOCCUS HORIKOSHII
    Organism Taxid53953
    SynonymADP-DEPENDENT PHOSPHOFRUCTOKINASE, ADP-PFK

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:35 , GLY B:118 , GLN B:119 , GLN B:246 , HOH B:1030 , HOH B:1033 , HOH B:1037 , HOH B:1092 , HOH B:1130 , HOH B:1241 , HOH B:1255BINDING SITE FOR RESIDUE SO4 B 1001
2AC2SOFTWAREARG B:334 , LEU B:335 , TYR B:417 , ARG B:421 , HOH B:1242BINDING SITE FOR RESIDUE SO4 B 1002
3AC3SOFTWAREASN A:35 , GLY A:118 , GLN A:119 , GLN A:246 , HOH A:1013 , HOH A:1021 , HOH A:1044 , HOH A:1133 , HOH A:1266 , HOH A:1396BINDING SITE FOR RESIDUE SO4 A 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U2X)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:33 -Tyr A:34
2Ala B:33 -Tyr B:34

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U2X)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADPKPS51255 ADP-dependent kinase (ADPK) domain profile.K6PF_PYRHO1-449
 
  2A:23-471
B:23-471
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADPKPS51255 ADP-dependent kinase (ADPK) domain profile.K6PF_PYRHO1-449
 
  1A:23-471
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADPKPS51255 ADP-dependent kinase (ADPK) domain profile.K6PF_PYRHO1-449
 
  1-
B:23-471

(-) Exons   (0, 0)

(no "Exon" information available for 1U2X)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:450
 aligned with K6PF_PYRHO | O59355 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:450
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450
           K6PF_PYRHO     1 MIPEHLSIYTAYNANIDAIVKLNQETIQNLINAFDPDEVKRRIEEYPREINEPIDFVARLVHTLKLGKPAAVPLVNEKMNEWFDKTFRYEEERLGGQAGIIANTLAGLKIRKVIAYTPFLPKRLAELFKKGVLYPVVENGELQFKPIQEAYREGDPLKINRIFEFRKGLKFKLGDETIEIPNSGRFIVSARFESISRIETREDIKPFLGEIGKEVDGAIFSGYQGLRTKYSDGKDANYYLRRAKEDIIEFKEKDVKIHVEFASVQDRKLRKKIITNILPFVDSVGIDEAEIAQILSVLGYRELADRIFTYNRLEDSILGGMIILDELNFEILQVHTTYYLMYITHRDNPLSEEELAKSLEFGTTLAAARASLGDIRGPDDYKVGLKVPFNERSEYVKLRFEEAKSRLRMREYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLEFLKRH 450
               SCOP domains d1u2xa_ A: ADP-specific phosphofructokinase                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -1u2xA01     1u2xA02 A:36-117,A:178-214  [code=3.30.1110.20, no name defined]                  1u2xA01 A:24-35,A:118-177,A:215-472                         1u2xA02 A:36-117,A:178-214           1u2xA01 A:24-35,A:118-177,A:215-472  [code=3.40.1190.20, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...eeeeeee.hhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh...eeeeehhhhhhhhhhhhh...eeeee....hhhhhh.....eeeeeee..eeeeee.hhh........eeeeeee....eeee..eeee....eeeeeee.hhhhhh......hhhhhhhhhhh..eeee.hhhhh........hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhh....eeeeeee...........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ADPK  PDB: A:23-471 UniProt: 1-449                                                                                                                                                                                                                                                                                                                                                                                                                               - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u2x A  23 mIPEHLSIYTAYNANIDAIVKLNQETIQNLINAFDPDEVKRRIEEYPREINEPIDFVARLVHTLKLGKPAAVPLVNEKmNEWFDKTFRYEEERLGGQAGIIANTLAGLKIRKVIAYTPFLPKRLAELFKKGVLYPVVENGELQFKPIQEAYREGDPLKINRIFEFRKGLKFKLGDETIEIPNSGRFIVSARFESISRIETREDIKPFLGEIGKEVDGAIFSGYQGLRTKYSDGKDANYYLRRAKEDIIEFKEKDVKIHVEFASVQDRKLRKKIITNILPFVDSVGIDEAEIAQILSVLGYRELADRIFTYNRLEDSILGGmIILDELNFEILQVHTTYYLmYITHRDNPLSEEELAKSLEFGTTLAAARASLGDIRGPDDYKVGLKVPFNERSEYVKLRFEEAKSRLRmREYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLEFLKRH 472
                            |       32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342|      352       362|      372       382       392       402       412       422       432       442       452       462       472
                            |                                                                           101-MSE                                                                                                                                                                                                                                           343-MSE             363-MSE                                                             431-MSE                                     
                           23-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:450
 aligned with K6PF_PYRHO | O59355 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:450
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450
           K6PF_PYRHO     1 MIPEHLSIYTAYNANIDAIVKLNQETIQNLINAFDPDEVKRRIEEYPREINEPIDFVARLVHTLKLGKPAAVPLVNEKMNEWFDKTFRYEEERLGGQAGIIANTLAGLKIRKVIAYTPFLPKRLAELFKKGVLYPVVENGELQFKPIQEAYREGDPLKINRIFEFRKGLKFKLGDETIEIPNSGRFIVSARFESISRIETREDIKPFLGEIGKEVDGAIFSGYQGLRTKYSDGKDANYYLRRAKEDIIEFKEKDVKIHVEFASVQDRKLRKKIITNILPFVDSVGIDEAEIAQILSVLGYRELADRIFTYNRLEDSILGGMIILDELNFEILQVHTTYYLMYITHRDNPLSEEELAKSLEFGTTLAAARASLGDIRGPDDYKVGLKVPFNERSEYVKLRFEEAKSRLRMREYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLEFLKRH 450
               SCOP domains d1u2xb_ B: ADP-specific phosphofructokinase                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -1u2xB01     1u2xB02 B:36-117,B:178-214  [code=3.30.1110.20, no name defined]                  1u2xB01 B:24-35,B:118-177,B:215-472                         1u2xB02 B:36-117,B:178-214           1u2xB01 B:24-35,B:118-177,B:215-472  [code=3.40.1190.20, no name defined]                                                                                                                                                                                          CATH domains
           Pfam domains (1) ADP_PFK_GK-1u2xB01 B:23-466                                                                                                                                                                                                                                                                                                                                                                                                                                 ------ Pfam domains (1)
           Pfam domains (2) ADP_PFK_GK-1u2xB02 B:23-466                                                                                                                                                                                                                                                                                                                                                                                                                                 ------ Pfam domains (2)
         Sec.struct. author ......eeeee...eeeeeee.hhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh...eeeeehhhhhhhhhhhhh...eeeee....hhhhhh......eeeeee..eeeeee.hhh........eeeeeee....eeee..eeee....eeeeeee.hhhhhh......hhhhhhhhhhh..eeee.hhhhh........hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhh....eeeeeee...........hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ADPK  PDB: B:23-471 UniProt: 1-449                                                                                                                                                                                                                                                                                                                                                                                                                               - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u2x B  23 mIPEHLSIYTAYNANIDAIVKLNQETIQNLINAFDPDEVKRRIEEYPREINEPIDFVARLVHTLKLGKPAAVPLVNEKmNEWFDKTFRYEEERLGGQAGIIANTLAGLKIRKVIAYTPFLPKRLAELFKKGVLYPVVENGELQFKPIQEAYREGDPLKINRIFEFRKGLKFKLGDETIEIPNSGRFIVSARFESISRIETREDIKPFLGEIGKEVDGAIFSGYQGLRTKYSDGKDANYYLRRAKEDIIEFKEKDVKIHVEFASVQDRKLRKKIITNILPFVDSVGIDEAEIAQILSVLGYRELADRIFTYNRLEDSILGGmIILDELNFEILQVHTTYYLmYITHRDNPLSEEELAKSLEFGTTLAAARASLGDIRGPDDYKVGLKVPFNERSEYVKLRFEEAKSRLRmREYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLEFLKRH 472
                            |       32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342|      352       362|      372       382       392       402       412       422       432       442       452       462       472
                           23-MSE                                                                       101-MSE                                                                                                                                                                                                                                           343-MSE             363-MSE                                                             431-MSE                                     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (K6PF_PYRHO | O59355)
molecular function
    GO:0043844    ADP-specific phosphofructokinase activity    Catalysis of the reaction: ADP + D-fructose 6-phosphate = AMP + D-fructose 1,6-bisphosphate.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008443    phosphofructokinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a fructose substrate molecule.
    GO:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0046835    carbohydrate phosphorylation    The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
    GO:0006000    fructose metabolic process    The chemical reactions and pathways involving fructose, the ketohexose arabino-2-hexulose. Fructose exists in a open chain form or as a ring compound. D-fructose is the sweetest of the sugars and is found free in a large number of fruits and honey.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        K6PF_PYRHO | O593553drw

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